VMD: a community annotation database for oomycetes and microbial genomes

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dc.contributor.authorTripathy, Suchetaen
dc.contributor.authorPandey, Varun N.en
dc.contributor.authorFang, Bingen
dc.contributor.authorSalas, Fidelen
dc.contributor.authorTyler, Brett M.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.date.accessioned2019-04-23T13:29:24Zen
dc.date.available2019-04-23T13:29:24Zen
dc.date.issued2006-01-01en
dc.description.abstractThe VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae and Phytophthora ramorum. With the completion of the draft genome sequences of these pathogens in collaboration with the DOE Joint Genome Institute (JGI), we have created this resource to make the sequences publicly available. The genome sequences ( 95 MB for P. sojae and 65 MB for P. ramorum) were annotated with similar to 19 000 and similar to 16 000 gene models, respectively. We used two different statistical methods to validate these gene models, Fickett's and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, we could assign putative functions to 17 694 genes in P. sojae and 14 700 genes in P. ramorum. We created an easy-to-use genome browser to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are similar to 1600 gene models for P. sojae and similar to 700 models for P. ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. The database is publicly available at http://phytophthora.vbi.vt.edu/.en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkj042en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.pmid16381891en
dc.identifier.urihttp://hdl.handle.net/10919/89094en
dc.identifier.volume34en
dc.language.isoen_USen
dc.rightsCreative Commons Attribution-NonCommercial 2.0 Genericen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.0/en
dc.subjectprotein familiesen
dc.subjectrecognitionen
dc.subjectinterproen
dc.subjectblasten
dc.subjectdnaen
dc.titleVMD: a community annotation database for oomycetes and microbial genomesen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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